Author: bugman
Date: Thu Dec 11 09:04:35 2014
New Revision: 27068
URL: http://svn.gna.org/viewcvs/relax?rev=27068&view=rev
Log:
Changed the argument order for the structure.align user function.
The standardised order will now be pipes, models, molecules, atom_id, etc.
Modified:
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27068&r1=27067&r2=27068&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 09:04:35 2014
@@ -105,19 +105,19 @@
print("Created the empty model number %s." % model_num)
-def align(pipes=None, molecules=None, models=None, method='fit to mean',
atom_id=None, centre_type="centroid", centroid=None):
+def align(pipes=None, models=None, molecules=None, atom_id=None, method='fit
to mean', centre_type="centroid", centroid=None):
"""Superimpose a set of related, but not identical structures.
@keyword pipes: The data pipes to include in the alignment and
superimposition.
@type pipes: None or list of str
+ @keyword models: The list of models to for each data pipe
superimpose. The number of elements must match the pipes argument. If set to
None, then all models will be used.
+ @type models: list of lists of int or None
@keyword molecules: The molecule names to include in the alignment and
superimposition.
@type molecules: None or list of str
- @keyword models: The list of models to for each data pipe
superimpose. The number of elements must match the pipes argument. If set to
None, then all models will be used.
- @type models: list of lists of int or None
+ @keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
+ @type atom_id: str or None
@keyword method: The superimposition method. It must be one of
'fit to mean' or 'fit to first'.
@type method: str
- @keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
- @type atom_id: str or None
@keyword centre_type: The type of centre to superimpose over. This can
either be the standard centroid superimposition or the CoM could be used
instead.
@type centre_type: str
@keyword centroid: An alternative position of the centroid to allow
for different superpositions, for example of pivot point motions.
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27068&r1=27067&r2=27068&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Thu Dec 11 09:04:35 2014
@@ -183,6 +183,13 @@
can_be_none = True
)
uf.add_keyarg(
+ name = "atom_id",
+ py_type = "str",
+ desc_short = "atom ID string",
+ desc = "The atom identification string.",
+ can_be_none = True
+)
+uf.add_keyarg(
name = "method",
default = "fit to mean",
py_type = "str",
@@ -191,13 +198,6 @@
wiz_element_type = "combo",
wiz_combo_choices = ["fit to mean", "fit to first"],
wiz_read_only = True
-)
-uf.add_keyarg(
- name = "atom_id",
- py_type = "str",
- desc_short = "atom ID string",
- desc = "The atom identification string.",
- can_be_none = True
)
uf.add_keyarg(
name = "centre_type",
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